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Old 03-18-2019, 04:50 AM   #666
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
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Quote:
Originally Posted by ssully View Post
How do I run the basic BBmap.sh script in Windows? What is the corresponding java command? I want to align four sets of paired-end Illumina RNA-Seq reads to a genome assembly. I am particularly concerned to correctly identify introns, as this genome is thought to have only a few intron-containing genes.

If your OS does not support shellscripts, replace 'bbmap.sh' like this:
Code:
java -XmxNNg -cp /path/to/current align2.BBMap in=reads.fq out=mapped.sam
(NN will be a real number on your system).
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